Finding the Connections Behind Hospital-Acquired Infections

Genomic surveillance can help infection prevention teams recognize related cases across units and procedures. Turning those findings into effective interventions remains the critical next step.

Matt MacKenzie

Nov. 10, 2026

6 min read

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Key Highlights

Hospitals often struggle to connect related infections due to their occurrence across different units and times, making traditional surveillance insufficient.
Genomic sequencing helps identify potential transmission clusters by comparing pathogen genetics, guiding targeted investigations and interventions.
Despite reductions in some infection types, pneumonia and surgical site infections remain challenging, highlighting the need for innovative prevention strategies.
Evaluating the success of prevention programs requires careful analysis of infection trends, staff adherence, and the impact of interventions over time.
Integrating environmental sampling and epidemiological data enhances understanding of infection reservoirs and transmission pathways, leading to more effective control measures.

Hospitals may identify an infection without recognizing the outbreak behind it.

Two patients can develop infections caused by closely related bacteria while receiving care in different units, undergoing procedures on different days, or encountering the same equipment without ever sharing a room. Each infection may be documented and treated, yet the connection between them can remain difficult to see.

For infection prevention teams, uncovering those connections can help answer an urgent question—where should they intervene to prevent the next case?

Healthcare-associated infections (HAIs) remain a substantial patient safety and operational challenge, even as hospitals make progress against some infection types. CDC findings released in July 2026 showed that, on any given day in 2023, approximately one in 38 hospitalized patients had at least one HAI, compared with one in 31 in 2015. The survey included 13,653 patients across 218 hospitals in 10 states. These figures describe the prevalence of infection on the survey day, rather than the percentage of hospital admissions that resulted in an infection.

The findings also illustrate where prevention challenges persist. Pneumonia, surgical site infections, and gastrointestinal infections were the most common HAIs identified. Overall, 61% were not associated with medical devices or operative procedures. CDC reported significant reductions in central line-associated bloodstream infections, catheter-associated urinary tract infections, and Clostridioides difficile infections, while pneumonia and surgical site infection rates showed little change.

For hospital leaders, those findings raise questions about how to build on established prevention programs while identifying risks that may be harder to recognize through existing surveillance practices. They also highlight the importance of looking beyond an organization’s overall infection count to understand which infections are occurring, whether cases are connected, and where additional resources could make a difference.

From identifying risk to demonstrating results

Determining whether a prevention initiative produces better outcomes can be challenging. Infection rates may already be changing before an intervention begins, and the effectiveness of a program can depend on how consistently staff incorporate it into their work.

A March 2024 study in JAMA Network Open examined implementation of a CDC C. difficile prevention framework across a regional hospital network. Twenty participating hospitals experienced steeper declines in hospital-onset infections than 26 comparison hospitals. However, infection rates at participating hospitals were already falling before implementation, and the rate of decline did not change during the intervention. The findings complicated efforts to determine the framework’s contribution.

A separate study, published in JAMA Network Open in June 2025, evaluated an AI-guided infection prevention bundle at Michigan Medicine. The program used electronic health record data to identify patients at elevated risk for C. difficile infection and guide enhanced hand hygiene and antimicrobial stewardship efforts.

Implementation was not associated with a statistically significant reduction in infection incidence. However, researchers observed reduced use of certain antibiotics associated with increased C. difficile risk. Their assessment also found differences in how staff used the interventions. Pharmacists consistently engaged with alerts, while adherence to enhanced hand hygiene protocols was poor.

Together, these studies highlight the work required to turn information into measurable improvements. Identifying risk is one step. Designing a response that staff can implement reliably, and evaluating whether it changes outcomes, requires additional attention.

Connecting cases through genomic surveillance

Genomic surveillance addresses another part of the prevention challenge and that’s determining which infections may be related.

By comparing the genetic sequences of pathogens recovered from different patients, investigators can identify potential clusters for further investigation. Medical records, procedure histories, patient locations, and other epidemiological information can then help teams examine possible shared exposures.

Environmental sampling can provide another layer of information when investigators are assessing potential reservoirs. Genetic findings must be interpreted alongside that broader evidence; a close match alone does not establish exactly how or in which direction transmission occurred.

Kurt Hackenberger, PhD, co-founder of Claryx, spoke with Healthcare Purchasing News about the gaps genomic surveillance aims to address and how investigators connect cases across a hospital. Claryx, a genomic surveillance company, uses pathogen sequencing and environmental sampling to help hospitals identify potential connections among infections and investigate possible transmission sources.

HPN: CDC found that 61% of HAIs identified in its survey were not associated with medical devices or operative procedures. What does that suggest about where hospitals should focus?

Hackenberger: Hospitals have built substantial infrastructure around preventing and tracking specific infections, including central line-associated bloodstream infections, catheter-associated urinary tract infections, and surgical site infections. That focus has been valuable.

The challenge is recognizing transmission that does not fit an obvious pattern. Two patients may enter through the emergency department, receive care in different parts of the hospital, and develop related infections. Their connection may be much harder to identify than a shared room or unit.

Comparing pathogens from patient infections can help investigators identify those connections. Depending on the investigation, environmental sampling may provide additional information about possible reservoirs. The goal is to give infection prevention teams a clearer picture of where to look.

HPN: How does genomic surveillance help investigators determine whether infections are connected?

Hackenberger: Sequencing allows us to compare the genetic makeup of organisms recovered from different patients. Closely related organisms can signal a potential transmission cluster that deserves investigation.

The next step is to examine the patients’ records and exposures. Did they share a room, undergo procedures involving the same equipment, or have another healthcare exposure in common?

The genetic information helps narrow the investigation. Patient records and other epidemiological evidence help investigators evaluate possible transmission routes and decide where to intervene.

HPN: Why might conventional surveillance identify individual infections without recognizing a shared transmission chain?

Hackenberger: Related cases may be spread across different units or separated in time. If investigators are primarily looking for an increase in infections within one location, those cases can be difficult to recognize as part of the same cluster.

Small clusters are particularly challenging. Two or three related infections may not produce an obvious increase above a unit’s usual infection count.

Genomic surveillance provides another way to identify cases that warrant investigation, including cases without an immediately apparent connection through shared space.

HPN: How should readers interpret the decline from approximately one in 31 hospitalized patients with an HAI in 2015 to one in 38 in 2023?

Hackenberger: Fewer healthcare-associated infections is an encouraging finding. The important distinction is that these figures describe how many patients had an infection on the survey day. They are not the percentage of admissions that resulted in an infection.

Interpreting changes over time also requires attention to how infections are identified and measured. For C. difficile, testing practices are relevant because detecting the organism does not necessarily establish that it is causing a patient’s symptoms.

The survey provides an important view of the overall burden. Hospitals also need to examine their own infection patterns and surveillance practices to understand where additional prevention work is needed.